Hi,
I have a problem with grompp.
I want to simulate membrane protein. I adjust the [ molecules ]
section to list the number and type of my components
I run grompp and it shows 56 warning about all of atom types in
ffG53a6nb.itp (56 atom types are in ffG53a6).
I run pdb2gmx for protein only
Hi,
Is there command in .mdp to adjust of frequency to write dg/dlamda to
dgdl.xvg file?
I do mdrun for 100 steps, so I get 100 dg/dl in dgdl.xvg file while
I want to change output to write 1000 dgdl in dGdL.xvg file. How can I do?
Thanks in advance.
thanks very much,
Afsaneh
--
gmx-u
afsaneh maleki wrote:
Hi,
I have a problem with grompp.
I want to simulate membrane protein. I adjust the [ molecules ] section to list
the number and type of my components
I run grompp and it shows 56 warning about all of atom types in ffG53a6nb.itp
(56 atom types are in ffG53a6).
Hi all,
I'm trying to run a parallel Job for a system of dummy atoms that arranged
as 2 surface (each is 6X6 atom surface- with bonds that i defined between
them)
the system is solvated in a box of dimensions 4.5nm X 6.5nm X 4.5nm with
salt, minimized and equlibrated fine.
however, when trying to
Amir Marcovitz wrote:
Hi all,
I'm trying to run a parallel Job for a system of dummy atoms that
arranged as 2 surface (each is 6X6 atom surface- with bonds that i
defined between them)
the system is solvated in a box of dimensions 4.5nm X 6.5nm X 4.5nm with
salt, minimized and equlibrated
For future reference, I was able to install gromacs and this is what finally
worked - installing gromacs in a folder different than the untared. It
somehow helped to not create the folder but just directly using the name in
the prefix
301 cd gromacs
302 ls
303 export CPPFLAGS="-I/fs/home/
Hi,
I'd like to ask the exact meaning of the bool variant bPBC, especially
in domdec.c. What does it exactly mean? It should relate to periodic
boundary condition I think. I had a system bounded by periodic boundary
condition on all 3 directions, and I used 4 nodes for simulation. The
system
Sai Pooja wrote:
For future reference, I was able to install gromacs and this is what
finally worked - installing gromacs in a folder different than the
untared. It somehow helped to not create the folder but just directly
using the name in the prefix
301 cd gromacs
302 ls
303 expo
Dear gromacs users:
I am confused (again) about pull_pbcatom0. From this analysis, I am
questioning if the pbcatom reported from grompp and in the top of the
.log file is numerically defined *within* a group or in the context of
the entire .gro file.
Either way, I think that I have conclu
I must remind you again that I am not your private tutor. Post all
Gromacs-related questions on the gmx-users list.
tekle...@ualberta.ca wrote:
Dear Justine,
if I want to restart my simulation (gromacs 3.3.3) do I need to
re-define the "init" and " init_step" respectively.For example if I
Sorry I just press the reply button and unfortunatley goes to you only.
regards,
Rob
Quoting "Justin A. Lemkul" :
I must remind you again that I am not your private tutor. Post all
Gromacs-related questions on the gmx-users list.
tekle...@ualberta.ca wrote:
Dear Justine,
if I want to
Hi all,
I am doing the umbrella sampling of a ligand pathway (Gromacs4.0.4).Now i
want to plot the PMF using WHAM analysis by Alan Grossfield. I installed the
WHAM program, read the manual too. But i am confused with the "loc_win_min"
and "spring" terms in the metadata file.
Can anyone please exp
loc_win_min is the center of restraint
spring is the force constant in kcal/mol (1000kJ/mol/nm^2 /4.184 = x
kcal/mol/nm^2)
You should probably read the manual again, this stuff is all there.
I'll not answer any further questions on this as (1) it's in Alan's
manual, and (2) this list is not
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